After traveling all night, 16 new competitors arrive in Panama City, Board the Rembrandt von Rijn still towing their bags, and, under the assumption that the upcoming Survivor: Pearl Islands starts in a few days, believe that they are sailing out to take publicity photos. Little do they know that it's already Day One, and they soon learn from Jeff Probst that in true pirate fashion, they'll be competing with just the clothes on their backs (with the exception of their running shoes for challenges). The castaways give Jeff their passports, jewelry, and any items that they don't want to lose, and are separated into two tribes named after two notorious pirates who sailed Panama's waters -- Henry Morgan and Sir Francis Drake. Wearing blue, the Drake Tribe consists of Rupert Boneham, Shawn Cohen, Jon "Jonny Fairplay" Dalton, Sandra Diaz-Twine, Trish Dunn, Christa Hastie, Burton Roberts and Michelle Tesauro. Wearing orange, the Morgan Tribe consists of Tijuana "T" Bradley, Nicole Delma, Darrah Johnson, Lillian "Lill" Morris, Ryan "Ryno" Opray, Andrew Savage, "Skinny" Ryan Shoulers and Osten Taylor. The two tribes then receive one bag of Panamanian money each and, after jumping overboard, head to an island where they find a Panamanian fishing village where must they pay and/or barter for the supplies they'll need for their adventure, keeping in mind that they must set aside enough money for boat rides to their respective islands, where they must be before sundown. After a tough loss at an Immunity Challenge, the Morgan Tribe goes to Tribal Council to vote off their first "pirate."
The Morgan Tribe was having a hard time sleeping during night 3, and this caused them to lose the Reward Challenge.
Drake won reward and won a piece of a map for their buried treasure. The Drake tribe also got to steal one item from the Morgan tribe. They sent Sandra and she chose to get their tarp, annoying the members on Morgan. Osten then told to the whole tribe that he wants to quit and Tijuana tries to calm him down.
Back at Drake, while fishing, Shawn loses the fishing spear which angers Rupert. So Rupert goes out on a search to look for the spear head and is successful.
At the Immunity Challenge, Morgan loses immunity and a 5-2 vote caused Ryan S. to be the second voted out.
At Morgan, morale is low as the tribe is suffering from two immunity loses. Lillian especially is down as she feels she has lost her best friend on the tribe, Ryan S., meanwhile Andrew thinks Osten needs to mentally toughen up.
Since Drake has their first clue, they decide to search for their treasure chest and have no luck. After the tribe gets tree mail, Sandra and Jon argue about who is the better swimmer between them. Jon vows Sandra won't be in the final four and definately won't win. The at the Reward Challenge, Morgan lose and Drake get blankets and pillows.
When Morgan wakes up the next day, Lill goes off fishing alone and Ryan O. feels the tribe should not spread out on its own. Lill returns from fishing empty handed and with a missing hook.
For the third time, Drake won the Immunity Challenge in a brawn testing battle, and Lillian, with all her efforts to stay in the tribe, got voted out.
The Morgan tribe wakes up the next morning and find that the ocean tide is rising and they need to adjust their shelter or make a wall to avoid the water. While at Drake, Jon continues to argue with his other tribemates. Christa and Rupert see the tension created by Burton and Shawn.
At the Reward Challenge, a sewing machine is up for grabs. During the challenge Osten can't handle the water and needs to be rescued by his tribemates and as a result Drake wins the sewing machine and a clue to find their treasure. Drake finds their treasure and although some things were moldy they were still able to get chocolate. Back on Morgan, Trish from the Drake tribe takes their lantern while Andrew and Ryan O. explore their beach in search for water and fish but find nothing.
During the night at Drake, Burton takes Rupert aside and tells him he thinks the tribe should purposely lose and vote out Christa and Trish. Rupert doesn't think it's a good idea but will do it anyway. Morgan wins the Immunity Challenge and a twist is introduced. Rupert is chosen by Morgan to join the tribe until the next Immunity Challenge. At Tribal Council it's between Christa or Burton.
With Rupert as a guest on the Morgan tribe, everyone helps move the shelter to avoid the tide. Over at Drake, the tribe miss Rupert and decide to leave their last can of Spam for when he returns. After the Reward Challenge he does, despite being offered a shower at the other tribe's beach. But when Drake loses the Immunity Challenge, Sandra and Michelle both feel they may be the ones leaving.
Rupert finds a wild snake.
Castaways previously voted off return to the game, creating a third tribe. Taking full advantage of their new opportunity, the "Outcast" tribe defeated both Drake and Morgan, forcing each of them to vote one contestant out of the game to make room for a returning outcast.
The Outcasts tribe vote back two players into the game - Burton and Lillian. The two report back to their original sides, who both act as though they are glad to see the previously eliminated person. The day after goes smoothly, even though Lill feels that her team is very lazy - and she is even more worried about her stay on the island...the Morgan tribe has run out of food. Thankfully, at the challenge the next day, the teams merge into the Balboa tribe, and after a win for Burton at the challenge, everyone goes back to the Morgan beach, where suspicions fly and both sides struggle to gain Lil's trust. At Tribal Council, Lill sides with the former Drake tribe by voting out Andrew, the obvious leader of the former Morgan tribe.
Everyone at Balboa is triumphant over Burton's latest catch -- an electric ray that all feast on. The next Tribal Council victim will also be the first juror to return to subsequent Tribal Councils.
A favorite player is voted out at a shocking Tribal Council.
On night 27 Christa is accused of sabotaging the fish food source by throwing them in the jungle. She swears she didn't do it, but she can't prove anything. Sandra tells us she did it. At the reward challenge, the survivors got to see their loved ones (moms, hubsands, fiances, etc). Jon receives news that his grandmother had died. The other survivor gave up their chance to see their loved ones so Jon could find out more about his grandmother. Jon and his buddy went back to Balboa Beach for 24 hours and the rest went to another beach for 24 hours. Back on Balboa, Jon jokes about how his grandmother didn't die and the fact everybody else believed him. At the Immunity Challenge, the survivors worked a puzzle where they form as many words from "SURVIVOR PEARL ISLANDS" as they can. Burton wins. As the survivors are leaving Jeff calls them back. Burton spelt a word wrong and was stripped of immunity. Lill, Darrah, and Sandra were left and got a new set of words. It was a timed trial and Darrah won Immunity with 14 words. At tribal council Jon's white lie went unknown as Tijuana became the 10th person voted out.
Lill, Jon and Darrah get treated at a hotel after winning immunity. Meanwhile back at camp, Christa tries to ally with Burton. All ends when Christa is voted off by everyone except Sandra.
With five left in the game, the competition becomes a battle of the sexes. While the two remaining men are away celebrating a reward that Burton won, the three remaining women hatch a plot against the men.
The Final Four castaways are reduced to two and the Jury votes for the winner.
Live from Television City in Hollywood, Jeff Probst tallies the jury's votes from Night 39 and announces the winner of "Survivor: Pearl Islands". Topics discussed during the reunion is the rumored-relationship between Burton & Michelle (which they deny), Rupert's love by fans (and the revealing of his sexy wife) and Jon's dead grandmother who seems to have come back from the dead for this show. The festivities conclude with Probst telling us about the upcoming "Survivor: All-Stars".